# Measure cluster colocalizations in spatialRNAseq with scRNAseq clusters

**URL:** <https://discourse.scverse.org/t/measure-cluster-colocalizations-in-spatialrnaseq-with-scrnaseq-clusters/1929>\
**Category:** squidpy\
**Created:** [December 1, 2023, 4:02pm UTC](https://discourse.scverse.org/t/measure-cluster-colocalizations-in-spatialrnaseq-with-scrnaseq-clusters/1929 "2023-12-01T16:02:36Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![gme](https://avatars.discourse-cdn.com/v4/letter/g/5fc32e/32.png) [@gme](https://discourse.scverse.org/u/gme)\
**Post date:** [December 1, 2023, 4:02pm UTC](https://discourse.scverse.org/t/measure-cluster-colocalizations-in-spatialrnaseq-with-scrnaseq-clusters/1929/1 "2023-12-01T16:02:36Z")

</div>

Hi,

I followed the scanpy tutorial to integrate scRNAseq clusters on spatial RNAseq samples. Now I am trying to measure the colocalization and the distances between these clusters on the spatial samples. I tried to use squidpy interaction\_matrix or nhood\_enrichment but it does not work, because the ‘leiden’ obs is lost after the integration of scRNAseq clusters using scanpy. Could you help me to fix it please?  
Thanks

---

<div class="post-metadata">

**Author:** ![gme](https://avatars.discourse-cdn.com/v4/letter/g/5fc32e/32.png) [@gme](https://discourse.scverse.org/u/gme)\
**Post date:** [December 13, 2023, 3:10pm UTC](https://discourse.scverse.org/t/measure-cluster-colocalizations-in-spatialrnaseq-with-scrnaseq-clusters/1929/2 "2023-12-13T15:10:55Z")

</div>

Hi, does anyone have any updates regarding this topic please?

Thanks